Ministry of Public Health spokesman Mohammad Ismaeel Kawosi told Anadolu Agency several people were also wounded in the attack.
There was no immediate claim of responsibility for the ambush but the Taliban has been involved in the previous four attacks on police and military bases this week.
It was the second suicide bombing in the Afghan capital in 24 hours and the seventh major assault in Afghanistan since Tuesday, capping one of the bloodiest weeks in the war-weary country in recent memory.
Daiul Haq Abid, spokesman for the Ministry of Haj and Religious Affairs, said that the death toll at the Imam Zaman Mosque rose to 54.
However No claim of responsibility has been made in the Ghor Mosque attack.
Almost 200 people, mostly security forces, have died in separate militant attacks across Afghanistan this week, making it one of the worst in recent months.
The attacks included assaults on a military hospital in Kabul in March which may have killed up to 100 people, and on a base in Mazar-i-Sharif in April which left 144 people dead.
Friday's attack on the mosques have been widely condemned.
Afghan officials said a suicide bomber detonated explosives inside the Shia mosque while an armed man opened fire there on Friday.
An attack on another Shiite mosque in the city on August 25 killed 28 people and wounded around 50 others.
A pro-government former Afghan jihadi commander reportedly was offering prayers along with his supporters when the bomber stormed the mosque.
In recent years, the Taliban and Islamic State jihadists have repeatedly targeted the minority Shiite community, who number around three million in overwhelmingly Sunni Afghanistan.